GENCODE: The reference human genome annotation for The ENCODE Project

By J. Harrow, Adam Frankish, J. Gonzalez, Electra Tapanari, Mark Diekhans, F. Kokocinski, Bronwen L. Aken, Daniel Barrell, A. Zadissa, S. Searle and 31 more. Genome Research, 2012

4,487 citations recorded by the source corpus.

The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5dcb131e1b335b14f712e31bc6a487e697f1b29b

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Citations in the corpus

GENCODE reference annotation for the human and mouse genomes (2018, background): “In 2007, we expanded our scope to the whole human genome as the ENCODE project did the same (4,5).”
LncRNA2Target v2.0: a comprehensive database for target genes of lncRNAs in human and mouse (2018, methodology): “To ensure data quality, lncRNAs were annotated by NCBI GenBank (31), Ensembl (32) and GENCODE (33), and each of these associations was double checked.”
ChIPBase v2.0: decoding transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data (2016, methodology): “We downloaded genome sequences and annotation sets of 10 species (human, mouse, rat, chicken, Xenopus tropicalis, zebrafish, worm, fly, yeast and Arabidopsis thaliana) from UCSC genome browser, GENCODE project (23) and Ensembl database (24) (Supplementary Table S1).”
Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci (2016, methodology): “We compiled a comprehensive catalog of human and mouse transcripts based on 1) Gencode annotation (Harrow et al., 2012); 2) human and mouse RNA-sequencing (RNA-Seq) from six matched tissues (brain, cerebellum, heart, kidney, liver and testis) (Brawand et al., 2011); and 3) RNA-Seq data from four…”
The Landscape of long non-coding RNA classification (2015, positive): “In fact, lncRNAs annotated by GENCODE - even those solely confined to intronic sequences - represent primarily spliced transcripts [33].”
ENCODE Data in the UCSC Genome Browser: year 5 update (2012, background): “The encyclopædia of genes and gene variants (GENCODE) gene set (11) is a fundamental resource produced by ENCODE, providing high-quality manual annotation from the Human and Vertebrate Analysis and Annotation (HAVANA) group merged with evidence-based automated annotation from Ensembl (12) across the”
Linking disease associations with regulatory information in the human genome (2012, methodology): “We use GENCODE v7 (Harrow et al. 2012) to identify SNPs that overlap transcribed regions.”
MIR sequences recruit zinc finger protein ZNF768 to expressed genes (2018, methodology): “Gene annotations were taken from GENCODE version 25 (41).”
Organoid profiling identifies common responders to chemotherapy in pancreatic cancer (2018, background): “p10 assembly) and obtained from GENCODE (release 27) (56).”
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression (2012, methodology): “…initial categorization of lncRNAs in the GENCODE gene annotation The lncRNA catalog described in this study represents a subset of the manually annotated GENCODE human gene annotation catalog (Harrow et al. 2012; www.gencodegenes.org/) that consists of 15,512 transcripts grouped in 9640 gene loci.”